{"id":"https://openalex.org/W1989334506","doi":"https://doi.org/10.1186/1471-2105-15-191","title":"Efficient design of meganucleases using a machine learning approach","display_name":"Efficient design of meganucleases using a machine learning approach","publication_year":2014,"publication_date":"2014-06-17","ids":{"openalex":"https://openalex.org/W1989334506","doi":"https://doi.org/10.1186/1471-2105-15-191","mag":"1989334506","pmid":"https://pubmed.ncbi.nlm.nih.gov/24934562"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-191","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-191","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-191","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-191","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033544261","display_name":"Mikhail Zaslavskiy","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mikhail Zaslavskiy","raw_affiliation_strings":["Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, 75013, France","Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, 75013, France","institution_ids":[]},{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030969222","display_name":"Claudia Bertonati","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Claudia Bertonati","raw_affiliation_strings":["Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, 75013, France","Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, 75013, France","institution_ids":[]},{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078915906","display_name":"Philippe Duch\u00e2teau","orcid":"https://orcid.org/0000-0002-3491-9168"},"institutions":[{"id":"https://openalex.org/I4210089315","display_name":"H\u00f4pital de la Croix-Rousse","ror":"https://ror.org/006evg656","country_code":"FR","type":"healthcare","lineage":["https://openalex.org/I4210089315","https://openalex.org/I4210100596"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Philippe Duchateau","raw_affiliation_strings":["Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris 75013, France. philippe.duchateau@cellectis.com","Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris 75013, France. philippe.duchateau@cellectis.com","institution_ids":["https://openalex.org/I4210089315"]},{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051541911","display_name":"Aymeric Duclert","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aymeric Duclert","raw_affiliation_strings":["Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, 75013, France","Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, 75013, France","institution_ids":[]},{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021831054","display_name":"George H. Silva","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"George H Silva","raw_affiliation_strings":["Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, 75013, France","Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, 75013, France","institution_ids":[]},{"raw_affiliation_string":"Research and Development department, Cellectis, 8 rue de la Croix Jarry, Paris, France","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5078915906"],"corresponding_institution_ids":["https://openalex.org/I4210089315"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4269,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.62744451,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"191","last_page":"191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.5605000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.5605000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0723000019788742,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.05510000139474869,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.8844696283340454},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6780915260314941},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5786548852920532},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5453583002090454},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.46676111221313477},{"id":"https://openalex.org/keywords/design-of-experiments","display_name":"Design of experiments","score":0.43189185857772827},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4282014071941376},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17401090264320374},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07156768441200256}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8844696283340454},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6780915260314941},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5786548852920532},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5453583002090454},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.46676111221313477},{"id":"https://openalex.org/C34559072","wikidata":"https://www.wikidata.org/wiki/Q2334061","display_name":"Design of experiments","level":2,"score":0.43189185857772827},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4282014071941376},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17401090264320374},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07156768441200256},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057166","descriptor_name":"High-Throughput Screening Assays","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-15-191","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-191","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-191","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24934562","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24934562","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3044288","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4065607","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-191","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-191","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-191","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4300000071525574}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1989334506.pdf","grobid_xml":"https://content.openalex.org/works/W1989334506.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1511037140","https://openalex.org/W1533491352","https://openalex.org/W1558918611","https://openalex.org/W1965802194","https://openalex.org/W1978129709","https://openalex.org/W1982969769","https://openalex.org/W2000046950","https://openalex.org/W2003171404","https://openalex.org/W2023490488","https://openalex.org/W2026410547","https://openalex.org/W2056026468","https://openalex.org/W2056833177","https://openalex.org/W2057896455","https://openalex.org/W2058304957","https://openalex.org/W2061460852","https://openalex.org/W2061492996","https://openalex.org/W2070493638","https://openalex.org/W2076282513","https://openalex.org/W2085277871","https://openalex.org/W2091219918","https://openalex.org/W2097360283","https://openalex.org/W2098398098","https://openalex.org/W2099438806","https://openalex.org/W2099862356","https://openalex.org/W2100475769","https://openalex.org/W2103622571","https://openalex.org/W2112291724","https://openalex.org/W2112985980","https://openalex.org/W2113927388","https://openalex.org/W2124241917","https://openalex.org/W2124538608","https://openalex.org/W2132207273","https://openalex.org/W2138883384","https://openalex.org/W2138973161","https://openalex.org/W2142068612","https://openalex.org/W2143116912","https://openalex.org/W2145193899","https://openalex.org/W2148504596","https://openalex.org/W2149310258","https://openalex.org/W2150798416","https://openalex.org/W2158698691","https://openalex.org/W2160095931","https://openalex.org/W2163296115","https://openalex.org/W2164852115","https://openalex.org/W2165618135","https://openalex.org/W3099289621","https://openalex.org/W4294541781"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4224009465","https://openalex.org/W4286629047","https://openalex.org/W4306321456","https://openalex.org/W160116885","https://openalex.org/W4285260836","https://openalex.org/W3046775127","https://openalex.org/W3170094116","https://openalex.org/W4205958290"],"abstract_inverted_index":{"BACKGROUND:":[0],"Meganucleases":[1],"are":[2],"important":[3],"tools":[4],"for":[5,54,93],"genome":[6],"engineering,":[7],"providing":[8],"an":[9],"efficient":[10],"way":[11],"to":[12,30,37,40,88,114,126],"generate":[13],"DNA":[14,43,96],"double-strand":[15],"breaks":[16],"at":[17],"specific":[18],"loci":[19],"of":[20,64,120,135,142],"interest.":[21],"Numerous":[22],"experimental":[23,80,127],"efforts,":[24],"ranging":[25],"from":[26],"in":[27,31,51,74,108,118],"vivo":[28],"selection":[29],"silico":[32,52,75,109],"modeling,":[33],"have":[34],"been":[35],"made":[36],"re-engineer":[38],"meganucleases":[39,57,92],"target":[41],"relevant":[42],"sequences.":[44],"RESULTS:":[45],"Here":[46],"we":[47],"present":[48],"a":[49,65,115,140],"novel":[50],"method":[53,101],"designing":[55],"custom":[56],"that":[58],"is":[59],"based":[60],"on":[61],"the":[62,121,133],"use":[63],"machine":[66,83],"learning":[67,84],"approach.":[68],"We":[69],"compared":[70,105],"it":[71,131],"with":[72,106,112],"existing":[73],"physical":[76,110],"models":[77],"and":[78],"high-throughput":[79,128],"screening.":[81],"The":[82],"model":[85],"was":[86],"used":[87],"successfully":[89],"predict":[90],"active":[91],"53":[94],"new":[95,100],"targets.":[97],"CONCLUSIONS:":[98],"This":[99],"shows":[102],"competitive":[103],"performance":[104],"state-of-the-art":[107],"models,":[111],"up":[113],"fourfold":[116],"increase":[117],"terms":[119],"design":[122],"success":[123],"rate.":[124],"Compared":[125],"screening":[129,136],"methods,":[130],"reduces":[132],"number":[134],"experiments":[137],"needed":[138],"by":[139],"factor":[141],"more":[143],"than":[144],"100":[145],"without":[146],"affecting":[147],"final":[148],"performance.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}